I’ve always known that there’s debate over whether Deckard is a replicant or not in the movie Blade Runner. I’ve never understood the debate because I feel the film spells it out pretty clearly. I figured some of the disagreement stems from people watching different versions of the film or the fact that some people just don’t pay much attention. I have friends who have movies as background entertainment, which is something I can’t do.

Today I was talking with a friend who had recently seen the best version (Final Cut, which is the true director’s cut) and they didn’t think Deckard was a replicant. So I explained why, in my opinion, he definitely is. I was surprised to find that two other friends, who also agree Deckard is a replicant, didn’t interpret the film the same way I did. I started asking my film friends online (ones I knew had seen the Final Cut) and none of them interpreted the film the same way I did.

I was a bit worried that I had read the film wrong. I took to Twitter and apparently only a small minority of followers seemed to know what I was talking about. So now I feel I have to dump these thoughts from my brain but I didn’t want to share all this in the Twitter thread because spoiling amazing films on social media isn’t a great idea. So here we go. Spoilers ahead. Seriously. Blade Runner (Final Cut) is a sci-fi masterpiece and really should be watched without spoilers so pleeeeeeeease watch it first before reading more. Here’s a nice picture before the spoilers begin.

Who is the “Blade Runner”?

The question “is Deckard a replicant or not” has always baffled me because it’s answered. To me the real question of the film that is eventually answered is “who is the Blade Runner?” I’ve always thought this was super obvious but the blade runner isn’t Deckard; it’s the ex-blade runner, Gaff. If you’ve forgotten who Gaff is, here’s a picture:

Yep, Gaff played by Edward James Olmos (also of Battlestar Galactica fame, so say we all). He is the super blade runner. The best there is. A legend. Let’s just be up front and tell you exactly what I thought was common knowledge by the end of the film: Gaff is the best blade runner but he’s getting older, he has a bad limp now and uses a cane, and just isn’t the “old blade runner” anymore.

What’s more, Tyrell can now create replicants who literally think they aren’t replicants by implanting them with the modified memories of real people. Rachel has the memories of Tyrell’s niece. I’m mostly ignoring the previous versions of the film but the original does mention that Gaff had been hanging around the Tyrell place and knew about Rachel. Of course he does. His memories have also been used in a replicant: Deckard.

“I need the old blade runner, I need your magic”

Blade Runner doesn’t have many characters who aren’t important to the plot. Sure there are extras roaming the streets but named characters with dialogue play an important part in the story. Except Gaff, apparently. He sits around and makes origami figures. But I think he’s the most important character in the film. The first time we see him he collects Deckard from a noodle bar. Unless Deckard has a tracker on it’s a bit weird that they find him there rather than his house or by calling him. Gaff knows where Deckard will be. This isn’t the last time Gaff appears to know what Deckard knows.

Next we see Gaff in the background as Deckard’s boss tries to give him an important assignment. Gaff doesn’t speak. He seems to have no role except to observe. It’s almost like he’s supervising. Or a backup if anything goes wrong with Deckard. I’m of the opinion that Gaff can still handle himself with a replicant. But four extremely dangerous models all at once? Sounds a bit much. When Deckard is refusing to take the assignment, Gaff knows he’s scared. Why? Because he’d be scared. Gaff knows Deckard better than anyone. That’s when he makes the first of his origami figures: a chicken. He also makes a man with a penis when Deckard is falling for Rachel and there’s the origami at the finale that we’ll get to. Is Gaff some kind of psychic?

There’s also a line from the boss that just stood out to me like a sore thumb. He seems excited and desperate to get Deckard on this case. Perhaps it’s a slip of the tongue but he says “I need the old blade runner, I need your magic”. Gaff, the best blade runner, isn’t his old self anymore. But with his memories in Deckard, maybe the old blade runner can be back in action?

“You’ve done a man’s job, sir!”

Gaff continues to keep an eye on Deckard, supervising him. It’s hard to know in the early stages of the film if this is a safety precaution in case Deckard figures out he’s a replicant or if Gaff is curious and sympathetic. But throughout we get hints that Gaff knows a creepy amount about Deckard. He knows where he’ll be, knows his emotions… and there are even more subtle clues but I won’t share too many because some could be coincidences. My favourite one that can’t be a real clue: I used to sell magic tricks for a living and the context I know the word “gaff” from is a gaff deck, a trick deck that looks like an ordinary deck of cards but is more than it seems. I’m sure it’s a coincidence rather than a hilariously clunky clue that the two characters are Gaff and DECKard!

But the film is full of hints that Deckard is a replicant. His journey through the film, discovering that Rachel is a replicant reflects our own journey as viewers learning that Deckard is. We’re introduced to Gaff first. We’re then introduced to the idea that replicants can think they’re human. We learn about false memories (and in some versions that Gaff has some involvement with the people who do this). Deckard comes to sympathise with Rachel and learn that replicants can feel and be loved, and we’re simultaneously learning this about Deckard. A really cheeky moment is when Rachel asks Deckard if he’s ever been tested himself and he falls asleep before he can answer. And that is the answer. It’s right there. If you want to know for certain if all these hints mean anything you have to look at that answer: his sleep.

Deckard has a recurring dream of a unicorn. There aren’t other unicorns in his life that we’re aware of. As viewers we are privileged to see Deckard’s dreams and know something that nobody else in his universe can know. We’re literally seeing into his mind. He dreams of unicorns. We learn this information and store it for later.

At the excellent climax of the film, the first person Deckard sees after Batty dies is Gaff. The original version of the film was very heavy-handed with its narration and also clues. For the better versions they removed the narration and some of the dialogue that made the plot too obvious. One of my favourite removed lines was Gaff’s compliment to Deckard: “You’ve done a man’s job, sir!” Oh my god, what a loaded line. Sure, he’s done a good job. And a man’s job. As opposed to what, a replicant? And not just any man’s job, but a specific man’s job! It works in so many ways.

Origami

But even then nothing is really confirmed. Gaff is always around, always supervising dealings with Deckard, always knowing where he’ll be… but it doesn’t confirm anything. Perhaps Gaff just has intimate knowledge of newer blade runners for professional reasons. But by this point of the film we also don’t have a solid explanation for why Gaff makes a chicken figure when Deckard is scared or a man with a penis when Deckard is talking about Rachel. That’s a little too intimate. Does Gaff know what Deckard is thinking? Yes. He knows because it’s what he’s thinking. Nobody knows Deckard like Gaff does. Actually, he even knows what Deckard dreams about because they share the same memories and dreams.

Gaff chooses to warn Deckard at the end of the film. He warns him to save Rachel and perhaps even protects her because he was at the apartment at the very end of the film. Then the film drops its big reveal: Gaff leaves his final origami figure for Deckard to find. A unicorn. The thing Deckard sees in his dreams. Why Gaff chooses to help Deckard isn’t explained. Maybe he becomes sympathetic for Deckard just as Deckard does for Rachel. It should be no surprise that they come to the same conclusion about the lives of replicants given that they’re more or less the same person. Deckard saves Rachel and Gaff saves them both.

This is my favourite thing in the film. The dream is such a great misdirection. Halfway through the film we see the dream as proof that Deckard is human. It throws us off the scent. I mean, do androids dream of electric sheep? But by the end it’s literally the answer to the big question of whether Deckard is a replicant or not.

That’s how I’ve always interpreted the film from the first time I saw it. I really can’t imagine seeing it any other way or Gaff would just be pointless. So there you go. I’m glad I got that out of my brain and onto the internet. I’m 100% positive others interpret the film the same way I do. They must do. But I’ve just been shocked at how many of my friends don’t see anything in Gaff when watching any of the versions including the Final Cut.

P.S.

I’m adding this short section just to address the reactions to this piece. I predicted I’d see a lot of people saying “oh wow yeah I know Deckard is a replicant but I never really thought about Gaff before except that he’s odd” and that is the most common reaction I’ve received. This piece is about Gaff, not about Deckard being a replicant. But I’m still getting reactions from people saying they think Deckard is a human and I’m not really understanding how they can explain that. You have another character aware of Deckard’s dreams. You have the director of the film confirming that Deckard is a replicant and that the unicorn is the reveal. And you have all the extra scenes that were cut because they would make it far too obvious. Try this alternative ending, for example:

“Did you know your wife for a long time?” is interesting because he answers “I thought I did”. It was actually Gaff that knew her. But more importantly this ending would make the very last lines of the film be: “We are made for each other”. That’s way too corny and heavy handed. I’m a big fan of how all the answers are in the film if you look for them but it’s much more subtle. I’m a huge fan of how making Deckard dream seemingly gives us proof he’s human early on and that someone else knows his dreams simultaneously shows he isn’t and makes the end of the film a callback to the title of Dick’s great book.

I think the real issue here is that Deckard is a human in the books and there’s a chance that Deckard may have been envisaged as a human in earlier versions of the film. I feel the character was always written to begin questioning it himself but in a subtle, vague way. So whether you think Deckard is human, or a replicant, or even perhaps the answer depends on the version you’re watching, you’re always supposed to at least have a suspicion and Deckard is always meant to have a vague sense of it regardless of the answer.

I’ve also had two reactions to the new film coming out. One is from people who feel Deckard is a replicant saying they were disappointed to see he’s still alive and that this is wrong or means they were wrong. The other reaction is from people who feel Deckard is a human, pointing to the new film as proof since he’s still alive. Remember, replicants live for four years.

So I hate to keep dragging you back to the original narrated version of the film because I don’t like how heavy handed it is but these are Deckard’s last narrated lines: “Gaff had been there, and let her live. Four years, he figured. He was wrong. Tyrell had told me Rachael was special. No termination date. I didn’t know how long we had together… Who does?”

Replicants live four years because they’re designed that way and you can’t change it or extend that life. But Rachel was designed to live longer. She’s special. She also differs from normal replicants in that she has the memories of a human (Tyrell’s niece). A replicant that has someone else’s memories and no forced termination date? Right there in the movies themselves? Maybe not so weird that Deckard is still alive in the new film, huh?

Late in 1999 I was feeling pretty lost. I had a good life by most measures but something was wrong. I’d felt it since childhood but when puberty hit, it went from “feeling different” to “the bad feeling”. Whenever I tried to bring it up with someone I was made to feel disgusting or broken. I’m transgender but back then I didn’t even know what to call it. Were there others like me? Was there something seriously wrong with me? Few things seemed to help but distractions such as videogames and films allowed me to briefly escape my feelings. In late September 1999 I rented a new sci-fi action film everyone was talking about. I pushed the tape into my trusty VHS player, huddled up in bed, and watched The Matrix for the first time.

In Neo I immediately saw a reflection of myself but I didn’t immediately read much into it. When you’re trans it’s easy to find characters to identify with because the transgender experience is a very human experience. A lot of trans people find characters to relate to in Disney, simply because many of their stories handle identity and being your true self. I saw Neo feeling lost, knowing that something was up but not even knowing what to call it. He would stay awake for hours at night on his computer, searching for answers, wondering if anyone out there felt like he did. I thought “here’s a character who feels lost like me” but I didn’t read more into it than that. Then the next scene spoke to me too. And the next. I started to have an unsettling feeling that this film knew more about me than I did, much like Neo watching someone else’s words flash across his computer. “Knock knock”. I’ve related to characters in films before but I got an eerie sense that The Matrix was created just for me. My heart was racing when Neo finally met Morpheus. Imagine baby trans Jen taking this in:

“You’re here because you know something. What you know you can’t explain, but you feel it. You’ve felt it your entire life, that there’s something wrong with the world. You don’t know what it is, but it’s there, like a splinter in your mind, driving you mad.”

What if I told you (in my best Morpheus voice) that The Matrix is a trans allegory touching on themes such as denial and acceptance of gender identity; trans erasure in death; the diversity of transition experiences (some people don’t use hormone therapy, others even regret transitioning); and that trans activism and education are necessary if we want to live in a peaceful world?

In the words of Neo…

Art isn't static

The film was written and directed by two trans sisters, Lana and Lilly Wachowski, who have stated that trans themes appear in much of their work but nowhere as obviously as in The Matrix. When asked about fans looking back at the film, with new knowledge that both creators are trans women, Lana Wachowski once said that “art isn’t static”. I couldn’t agree more and this really gets to the heart of why I want to write this piece.

Viewing art with a fresh pair of eyes can be like experiencing it for the first time all over again. Consider the many different perspectives people could have when viewing The Matrix. It’s obvious that a cisgender person (someone who isn’t trans - these are Latin prefixes), will likely interpret the film differently than a trans person would. Perhaps you may interpret the film differently before compared with after learning that the Wachowskis are trans women. Of course some people can’t see it at all:

For me, always watching as a trans person, the interpretation of the film has evolved just as I have over the years. Art isn’t static. Of all the themes and metaphors you will read in this piece, I think I recognised about 25% of them during that very first viewing in my bedroom as baby trans Jen. I saw things that my friends didn’t, because they had no trans experience whatsoever. Over the years I’ve gleaned more and more from the film because of my own personal journey. As I grew up I learned trans terminology; I learned there were others like me; I learned about hormone replacement therapy; I learned about haters, chasers, and allies. As my own trans experience evolved, I noticed more of the trans allegory in scene after scene until the film became a living, breathing thing that changed alongside me.

Another reason for emptying these thoughts onto the internet is because I disagree, on many points, with others who have covered it before. I read some of the characters and scenes very differently. More importantly, I don’t think the trilogy has been given enough attention as a trans allegory. When viewed as generic sci-fi action films, the sequels really don’t do the original justice. As a trans allegory, however, they build on the original brilliantly and I think the people who miss the allegory also miss what makes the sequels interesting. Indeed, I believe many aspects of the sequels don’t make sense unless viewed as a trans allegory. I believe this is worth looking at closely and discussing further.

In order to share what I’ve taken from the film I need to provide a little perspective, so this piece necessarily has to touch on personal stories too. My goal is to give you some insight so that you (especially if you’re cisgender) can empathise and see why the film speaks to me and many other trans people. This might not be your average film analysis (actually it’s best to just consider this venting) but stick with me and and I’ll show you how deep the rabbit-hole goes.

Plugged into the cis-tem

Neo is obviously at the core of The Matrix. In the trans allegory, his journey to become “the One” is also his journey to become his true self. Whether you’re following the sci-fi plot or the trans allegory, Neo starts by knowing there’s something up, though he doesn’t know exactly what. There’s definitely more to his world. Then he comes to learn what he is by meeting other people who also felt the way he does. That doesn’t necessarily mean he accepts it or fully believes it himself. He has forces in his life that believe in him and others that threaten him, but through struggles Neo comes to accept himself and who he really is. This arc, taking Neo from discovering the truth to accepting his identity, takes place over the entire first film. The sequels handle the necessity of activism, the diversity of transitioning experiences, and peace.

“The Matrix is a system, Neo. That system is our enemy. But when you’re inside, you look around, what do you see? Businessmen, teachers, lawyers, carpenters. The very minds of the people we are trying to save.”

In the film, the matrix itself is one of two worlds or more accurately a world within a world. In the trans allegory, the matrix is simply how society sees gender. The matrix is cis-normative society. As Morpheus explains, that world or way of thinking is all around us. We see it on TV and we see it when we look out the window.

It’s no accident that the matrix was created by machines. It’s artificial. It’s a construct. All the humans living in the matrix are real biological beings trapped into thinking of gender in its most simplistic terms - not recognising trans people, and not recognising gender beyond the binary. Trans people break free from this system, which is represented in the film by our heroes being unplugged from the matrix itself.

“You have to understand, most of these people are not ready to be unplugged. And many of them are so inured, so hopelessly dependent on the system, that they will fight to protect it.”

Importantly, the cis people obliviously walking around in the matrix are not the enemy; the system is the enemy. There are people out there who say that Black Lives Matters is anti-white, or feminism is anti-men, and that’s obviously bullshit. Similarly, being a trans allegory doesn’t make The Matrix anti-cis. In fact, the allegory paints cis people as victims in this system too, and that — ultimately — peace comes from understanding and cooperation between trans and cis people.

“It is the world that has been pulled over your eyes to blind you from the truth.”

“What truth?”

“That you are a slave, Neo. Like everyone else you were born into bondage. Into a prison that you cannot taste or see or touch. A prison for your mind.”

The earliest scenes in the film are the most obvious, even to cis people. When Neo begins his journey he is given a choice between the red pill or the blue pill. Many trans people take pills as part of their hormone replacement therapy during transitioning. The fact that assholes online have accidentally co-opted the red pill from a trans allegory created by two trans women is both disappointing and unintentionally hilarious. Side-note: It’s important to note that some trans people don’t undergo hormone replacement therapy (HRT) and they are just as valid as trans people. The Wachowskis address this brilliantly in the sequels and anime projects through Kid, a character who wakes himself up from the matrix without the aid of any pills at all. In the allegory, he’s a trans person who accepts himself and transitions without HRT. He looks up to his trans heroes and he’s one of them without taking any pills. But I digress, we’ll get to the sequels another time.

These Morpheus quotes I’ve been using come from a training scene where Neo learns about agents. It’s extremely powerful but I don’t believe it hits as hard for cis people. The agents are the real enemy. They’re a consequence of the system. They represent fear and hatred of the people unplugged. They’re the oppression of trans people. You can think of them as actual individuals in the sense of transphobic bigots but in the allegory they also represent that fear and hatred as a concept.

I’ve watched many films that openly feature trans people and no other has so accurately captured the feeling of walking down a busy street as a trans person. When I walk into town I know that most of the people around me are good, decent people. Most would probably come and help me if I was attacked or hurt. However, it’s also a fact that an alarming number are hostile to trans people. At best they might ridicule me; at worst they might try to murder me. The terrifying thing is that transphobes don’t have signs hovering above their heads. Until they actually attack, they look just like everyone else. They blend in. When you walk through a sea of people, you have no idea who could really be filled with that hatred, so you have to be ultra vigilant around everyone.

You don’t know who could be an agent.

Trans stories

Neo is the core of the trans allegory but the cast he meets are equally important. Some of them represent aspects of his own journey (especially Morpheus and Agent Smith, who we’ll come to) but other characters tell specific trans stories.

There’s Switch, the only character who was specifically written as transgender. She’s the embodiment of the allegory; of being unplugged. Originally the role was to be performed by two actors, one male and one female, to give her a different body when inside or outside the matrix. The sci-fi aspect here is that there’s a glitch in the matrix that left her with a mental projection that doesn’t match her gender. (I’m going to continue using she/her pronouns for Switch because it’s canon now and you know who I’m talking about).

The production companies didn’t like this and had the Wachowskis play down the trans aspect and have the character performed by one actor. The Wachowskis compromised in several ways. Firstly, they hired an androgynous actor, which is probably the next best thing. Most importantly, they kept her character the same. We still know her as Switch, a name that references the switching between bodies as she plugs in and out of the matrix. She even keeps the white clothing while everyone else wears black; a visual queue to help viewers realise the two appearances in the original vision are the same character. Even better, she keeps her original dialogue. Her death scene isn’t exactly nonsensical, but it makes much more sense when you realise that the Wachowski’s engineer a scene in order to talk about trans erasure in death.

Many people come out to find that their relatives and loved ones are unsupportive or even hostile to trans people. It’s also a fact that a scary number of trans people die each year, sometimes from suicide or murder. Sadly, many of these unsupportive families erase the dead’s identity by deadnaming them and ignoring their transness. Obituaries and gravestones show deadnames. This is really common. In the allegory, the Wachowskis give these dead people a voice by engineering a situation where Switch knows she’s about to die. So there she is: back in the world she tried so hard to escape from, and in the body she tried so hard to escape from. Her last words might as well be those of all the trans people who have had their identity erased in death. “Not like this. Not like this.”

The biggest disagreement I have with others is over Cypher, who most people interpret as a chaser. I can see where this thought comes from as he hangs around the heroes, uses them, turns on them, and there’s clearly attraction involved with Trinity. I feel this oversimplifies one of the best characters in the film and a big part of the allegory. I think this view falls down when you consider that Cypher is unplugged, like the others, so he’s a trans person who has transitioned. The difference is that he’s unhappy. He’s jealous of others around him like Neo. And most importantly, he’s filled with regret. He doesn’t like this new world he finds himself in and wants to go back. Just as the sequels bring up more nuanced issues like transitioning without hormone therapy, the original film brings up the fact that there are people out there who wish to detransition.

The most striking parallel with Cypher’s story and our world is that many people who detransition are used by transphobes in order to attack trans people further. People who detransition are seen as proof that there’s something wrong with being transgender or that society is forcing people to transition when they clearly don’t need to. Lo and behold, the agents use Cypher’s detransition back into the matrix to get to the heroes. They capitalise on his struggle. They appear as his allies but ultimately use him to deal a blow to the community he wishes to leave. We’re watching real-life play out on the Nebuchadnezzar.

The worst part of yourself

Not all agents are born equal and Agent Smith plays a very special role in the The Matrix as both a film and a trans allegory. He’s unique, even as an agent. He does represent fear and hatred of trans people just as the other agents do, but for him it’s also self-hatred. As the Oracle eventually explains, Agent Smith and Neo are one and the same. They are flip sides of each other. Two halves of an equation. Equal yet opposite. Agent Smith is a failed “One” while Neo goes on to become successful. In the allegory, Neo eventually comes to accept his trans identity but Agent Smith does not. In some ways you can view Agent Smith as his own person, like a self-hating trans individual, but in almost every scene he also acts as a fearful, hateful aspect of Neo himself.

Being another agent, Smith always represents hostility towards trans people, but he clearly plays by his own rules and has his own purpose. Every action he takes represents Neo’s fear and doubt. Whenever he speaks to Neo, he deadnames him. Always Mr Anderson; never Neo. He captures and tortures Morpheus, who represents the hope and belief Neo has in himself (I’ll get to that). Agent Smith is the part of you that tries to keep you down, sow seeds of doubt, and tell you what isn’t possible. Your failure is inevitable.

Let’s step back from the film for a moment and talk about something that really happened. Content warning: contemplation of suicide. Years before filming The Matrix, Lana Wachowski hit an all-time low in terms of gender dysphoria and willingness to accept herself as trans. She decided to take her own life by walking down into a subway and jumping in front of an approaching train. She fought with herself and at the last moment changed her mind. Down there in the subway, she accepted her identity and from that moment knew she could live a genuine life as her true self. Facing your darkest self in a subway sounds familiar, no?

For my teenage friends, back in 1999, the subway scene was just another great moment of action; but for trans viewers it’s the emotional crux of the film. Neo is being hunted relentlessly by agents and comes face to face with Agent Smith, where he is pinned and appears doomed to be hit by the incoming train. Agent Smith, deadnaming Neo as usual, describes his death as inevitable. The train is coming and one way or another, “Mr Anderson” is going to die.

“My name… is Neo.”

Up until this moment Neo has been struggling to believe in himself and accept who he is. He clearly wants to believe but with so many forces against him it’s difficult. In this scene, like Lana Wachowski when she was in the real-life subway, Neo finds the bravery to fight for his life and begin accepting himself. As Morpheus says, “he’s beginning to believe”.

While Smith can be seen as the part of Neo that is self-hating and scared, Morpheus is the part that believes in himself. It’s no accident that many of the challenges Morpheus faces are from people who simply ridicule that belief. Just as in real life, transphobia comes in different forms. It’s true that trans people face violent hatred in the real world but we also face more subtle, casual transphobia and doubt from people close to us. Many attacks from transphobes are forms of emotional abuse. Some of the characters in this fictional universe aren’t violently aggressive towards Neo but they clearly have strong opinions about whether or not Morpheus is insane for believing in the One. I’m also often told I’m insane for being trans.

If Agent Smith is the part of Neo trying to get him to give up, Morpheus is the part that knows the truth deep down. For me Morpheus represents belief either in yourself or belief and support from others. He picks you up when Smith knocks you down. This is an area where I disagree with others who have written about the trans allegory. Most writers see Morpheus as an older, wiser trans person who gives guidance. (If anyone plays that role I believe it’s the Oracle, who has some answers but insists you have your own story to understand). Agent Smith tells you that what you’re doing is impossible. Your failure is inevitable. When Smith is the voice saying you can’t do it, Morpheus is the voice saying you can.

Why do you persist?

When I started typing this piece I envisaged a well-structured article covering the entire trilogy. Instead it turned into this rambling outpouring of opinions mostly about the first film. I’m OK with that. I see personal pieces like this as entries in a diary of sorts. This is what I think about The Matrix. If anyone else gets something out of it then that’s cool. As a way for me to get my thoughts about the film out of my head, I’ve achieved my goal. I feel I’ve vented. I wanted to bring up a few aspects where I disagree with others and I did that. Mission accomplished. I feel better now. Ahhhhh.

That said, maybe you want more from this. Maybe I should really dive into the film properly. Maybe I should put my money where my mouth is and cover the continued trans allegory present in the sequels. Maybe. I’ll think about it. If there’s some demand, I could create a series of articles looking at each film individually. I am genuinely surprised that more people haven’t considered the sequels as continuations of the allegory. I’ve tried to watch them and focus on the sci-fi story alone, ignoring any hints of trans stories, and they’re really quite pointless. Perhaps I can help you enjoy them more by providing some of this context in a future entry, because both sequels are infinitely more rewarding when viewed through the lens of a trans person.

Neo’s journey to become his true self is fantastic but so is his wider journey as an activist fighting for other trans people. I actually like the sequels and the direction they take the allegory. The first film finishes in the most perfect way for a continuation about becoming an activist and fighting for other trans people. When Neo talks directly to the machines at the end of the film, he’s talking directly to the hateful transphobes and people obsessed with enforcing the gender binary.

“I know that you’re afraid… you’re afraid of us. You’re afraid of change. I don’t know the future. I didn’t come here to tell you how this is going to end. I came here to tell you how it’s going to begin. I’m going to hang up this phone, and then I’m going to show these people what you don’t want them to see. I’m going to show them a world without you. A world without rules and controls, without borders or boundaries. A world where anything is possible. Where we go from there is a choice I leave to you.”

I’m not the biggest fan of action films but The Matrix means a lot to me. My friends tell me I’m brave just for being myself. I get death threats because of my gender. I’ve been assaulted for it. I’m violently hated by transphobes including some who stand against racism, homophobia, sexism etc. Every walk down the street requires extreme vigilance. Society seems determined to stop me, just like the forces standing against Neo. This is what makes him a brave hero for many trans people. He could take the easy way out at any opportunity but instead gets right back up every time he’s knocked down. In the climax of the third film, Agent Smith is sure he’s beaten Neo for good only to see him stand up once more. Agent Smith is the worst part of Neo. Deadnaming him again, Agent Smith asks the question that the worst part of me has asked myself far too often in the past:

“You must be able to see it, Mr. Anderson. You must know it by now. You can’t win. It’s pointless to keep fighting. Why, Mr. Anderson? Why? Why do you persist?”

“Because I choose to.”

These are hastily typed thoughts on The Matrix as a trans allegory. If there’s any interest I would be happy to create a series of articles covering the entire Matrix trilogy and touching on the Animatrix.

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Nice Trump is a simple Chrome extension for Twitter, which replaces Donald Trump's tweets with nice and interesting facts about the world.

If you don't like Trump's tweets you could just mute him, but using this extension means you'll get periodic reminders that the world can be pleasant whenever someone

Nice Trump is a simple Chrome extension for Twitter, which replaces Donald Trump's tweets with nice and interesting facts about the world.

If you don't like Trump's tweets you could just mute him, but using this extension means you'll get periodic reminders that the world can be pleasant whenever someone retweets Trump into your timeline.

If you MUST see what Trump is tweeting then permalinks will still show the original content of his tweets. Only tweets in timelines or on his profile page will show up as Nice Trump tweets.

Today I made a Twitter account, @GifEarth, that shares (almost) daily GIFs of our planet as it looks from deep space approximately a million miles away. Here's an example of the content it shares (from 2016-10-20):

I like that one so much, I used it as the profile picture for @GifEarth. This Twitter bot checks with NASA to see if there are any new images for the day. If so, it collects all of them together, formats them and adjusts their sizes in order to make an animation small enough for Twitter. It combines all the images together to make one GIF for the whole day and uploads it as a tweet.

I'm fascinated by autonomous vehicles and do my best to keep an eye on what's happening worldwide. This morning I was told by Baidu USA that the state of California's Department of Motor Vehicles has given Baidu permission to test autonomous vehicles on their roads. Jing Wang, General Manager of

I'm fascinated by autonomous vehicles and do my best to keep an eye on what's happening worldwide. This morning I was told by Baidu USA that the state of California's Department of Motor Vehicles has given Baidu permission to test autonomous vehicles on their roads. Jing Wang, General Manager of Baidu's Autonomous Driving Unit, made the announcement:

We will start testing our autonomous driving technologies on public roads very soon in California.

Baidu has already built a strong team in Silicon Valley to develop autonomous driving technologies, and being able to do road tests will greatly accelerate our progress.

Baidu USA (the US branch of the "Chinese Google") had already announced that they were developing autonomous vehicles. The big news is that they're making steady progress in the US and now have permission to test on Californian roads.

We have recruited top researchers and engineers to join our team, and look forward to recruiting more people to work on the mission of bringing autonomous cars to the masses in the near future.

I'm less interested in what this means for competitors in the US such as Google and far more interested in what it means for the car manufacturers that aren't keeping up. It looks like many of the big players will be companies known for AI or internet services (Baidu, Google, Uber etc) but companies like Ford are working hard to stay ahead.

What happens to the other manufacturers if they don't adapt quickly? If autonomous vehicles become the norm they could find themselves providing hardware for Baidu and others already in the self-driving game.

We're in for an exciting decade or two.

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A few years ago I got bored one evening and coded a Twitter bot that generates New Scientist-headlines, as seen on Buzzfeed and featured on New Scientist itself. I do like New Scientist and I was just taking the piss out of the more sensationalist headlines. I realised that the

A few years ago I got bored one evening and coded a Twitter bot that generates New Scientist-headlines, as seen on Buzzfeed and featured on New Scientist itself. I do like New Scientist and I was just taking the piss out of the more sensationalist headlines. I realised that the funniest tweets were the surreal ones so I gave it permission to experiment a bit more with bizarre headlines and made it learn what people liked based on retweets and favourites. After 1000 tweets and 900+ followers I chose to retire it. But now it’s back!

BREAKING: An unusual radio wave from a nearby galaxy suggests that Hillary Clinton's eyebrows are on point

Cars are increasingly becoming electric and we're all wondering if autonomous vehicles will really take over the roads within the next decade. It's an exciting time for the transport industry but some car manufacturers will be understandably nervous. As the industry becomes more software-driven, traditional manufacturers run the risk of

Cars are increasingly becoming electric and we're all wondering if autonomous vehicles will really take over the roads within the next decade. It's an exciting time for the transport industry but some car manufacturers will be understandably nervous. As the industry becomes more software-driven, traditional manufacturers run the risk of becoming a mere supplier of car shells as technology changes our cities and transport infrastructure.

I've asked several Ford project leads about the future of driving and always get the same answer: we're moving into a world where cars will be smart, connected, autonomous, and work with big data from connected city-wide systems. Ford aren't alone in making their cars autonomous but they certainly stand out when it comes to thinking about how we use transport.

Scoring your behaviour

At a London Tech Week panel on “Changing the way the world moves”, Ford continued to showcase experiments under their Smart Mobility Plan. It's not about making the next great car; it's about being a transport leader as technologies change how we commute and travel. The big reveal this week was their Driver Behaviour Project: an experiment that gives drivers a personal score based on their driving behaviour.

The score is calculated based on how you drive but also how you feel. Hardware in the car monitors both the handling of the car and also your eye movements, voice, facial expressions, and heart rate. All this data is brought together by an algorithm that gives you a driving score. The higher the score, the better you are at driving (“better” meaning safe and efficient as opposed to being a Mario Kart superstar).

While the data would obviously be useful to Ford's engineers and scientists, they claim the data belongs to the driver and is designed to empower them. A good driving score could result in discounts for car rental, insurance, or car-sharing services.

You check your score on a smartphone app, which feels similar to the empowerment and gamification that works well in fitness apps and might have the same effect on behaviour. Instead of helping lose weight or gain muscle, the driving score could help you make savings by becoming a better driver.

“Like an activity-tracking app that shows the distance we cover and calories we burn, a personal driver score encourages people to drive smarter,” said the project lead, Jonathan Scott. “We wanted to better understand how people use our products so we could help them to improve that behaviour – and a score, combined with guidance, makes it easier to improve.”

The London commute

The Driving Behaviour Project started with an 4-month experiment monitoring drivers in London. Volunteers drove over 40 Ford Fiestas around London for a total of 4,000 hours and 160,000 km. During this time, the drivers' eye movements and heart rate were recorded. A small device also collected data from the cars themselves such as speed, steering, braking, and combined the data with the time of the day, weather, and even the road history.

Steady acceleration and smooth steering results in a higher driving score. The smartphone app makes suggestions to help improve your driving such as staying in the correct gear while graphs show daily scores so drivers can figure out if they're better at driving on specific days. Perhaps the heavy traffic at certain times has an effect on your mood and driving behaviour.

The 4-month experiment was primarily to create the driving score algorithm but the science didn't stop there. Ford is now working with the University of Nottingham to study driving stress by monitoring drivers during difficult situations inside a driving simulator, which was also available to try at the London Tech Week event. The heart rate, eye movements, and brain imagery of volunteers were monitored during simulations of heavy traffic and when large vehicles block vision. These situations tend to make drivers more nervous and stressed. It's hoped that a better understanding of how driving affects us physically and emotionally can help us become better drivers.

While many of Ford's most exciting Smart Mobility plans are years away, the driving score could soon be implemented into current on-demand car and ride-sharing services like GoDrive and GoRide.

Other Smart Mobility projects

The Driver Behaviour Project is just part of Ford's Smart Mobility vision at London Tech Week.
They also showed off several new services including GoPark, a smart parking system. With hardware plugged into participating vehicles, a probability-based algorithm will let drivers know the odds that there will be a free parking space at their chosen destination. Obviously this is the type of service that will only work if there are a lot of participating vehicles so Ford might want to implement this into all their future models if the demand is there.

Moving beyond what was seen at London Tech Week, Ford's vision for Smart Mobility is ambitious and other experiments include data-driven insurance, remote repositioning, car swaps, Info Cycle, and data-driven healthcare in remote areas of West Africa. Technology is changing driving and Smart Mobility is how Ford aims to drive change rather than adapt to it. They're already one of the leaders in autonomous driving with purpose-built cities for testing the vehicles and their current models can now read traffic signs and see around corners.

Over the next few years we should start to see more advances in car technology that rely on software as much as hardware. Just last month Ford invested $182.2 million in Pivotal, a cloud-based software company that will develop Ford's software and analytical tools for Smart Mobility experiments.

Ford wants to be ready should we choose to forgo owning our cars or even driving them ourselves. It's a future that might scare die-hard driving fans but they won't want to get too excited behind the wheel; it might affect their insurance policy.

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Emma Boyle is a gaming, technology, and fashion writer. I created emmaboylewrites.com as a place to find her contact information and some examples of her writing. The website is responsive and works well on small touchscreens as well as wide desktop monitors.

Emma Boyle is a gaming, technology, and fashion writer. I created emmaboylewrites.com as a place to find her contact information and some examples of her writing. The website is responsive and works well on small touchscreens as well as wide desktop monitors.

I practically live on Twitter. Jen's Butler is an interactive Twitter bot that allows me to do nearly anything without leaving Twitter. The butler can access online services I use, retrieve files I store locally on various computers, and control connected devices in my home.

I practically live on Twitter. Jen's Butler is an interactive Twitter bot that allows me to do nearly anything without leaving Twitter. The butler can access online services I use, retrieve files I store locally on various computers, and control connected devices in my home.

The butler accesses services in two different ways. Most of the functionality comes from the Python script that generates the tweets. This script also calculates astronomical predictions, works with local files, edits images, controls security equipment connected to a Raspberry Pi, and many other actions. The rest of the functionality comes from IFTTT such as providing sports scores.

Update: This post was just a quick rant. If I knew it would become so popular I would have put in more effort. I get so many emails about this piece and it gets linked to so often that it just goes to show how much of a problem this is in education. I'm glad it's helping people.

This is a big pet peeve. Let’s get straight to business: the terms “homeobox” and “Hox” are not interchangeable. They do mean different things. I’m correct in saying that Amphioxus (Branchiostoma lanceolatum) has 15 Hox genes. I’m also correct in pointing out that it has over 130 homeobox genes.

Gene names can be very confusing and difficult to remember, so there are many abbreviations in biology. For example, the gene insulin-like growth factor 1 is abbreviated to Igf1. Does that make it easier to remember? Who knows. But I believe the use of abbreviations is partly responsible for the incredible confusion over homeobox and Hox genes. And I do mean incredible. It’s very obviously a confusing topic for students, or anyone new to evo-devo, developmental genetics, or gene regulation… but it’s so much worse than that. Professional publications make the mistake, academics make the mistake, and they do it often. I think the reason it keeps happening is that the word “Hox” appears to be a shortened “Homeobox”. All over the internet you will see the terms used interchangeably, and sometimes with the apparently shortened version in brackets. “Homeobox (Hox)”. This otherwise decent glossary at Epigenesys manages to dump the terms homeotic, homeobox, and Hox into one single paragraph and glossary entry, which is of little help to a confused student seeking clarity. The first Google result for “homeodomain” (ignoring Wikipedia) is R&D Systems saying, “The DNA sequence that encodes the homeodomain is called the ‘homeobox’ and homeobox-containing genes are known as ‘hox genes’. This is wrong. A homeobox-containing gene is not necessarily a Hox gene. So let’s clear this up and I’ll keep it quick.

First, let’s go over the facts, and the answer, before we discuss why these confusing names have been chosen. Scientists discovered that there are some genes that contain a very conserved region of DNA we now call the homeobox. When I say very conserved, I mean it. You have homeobox genes, the birds outside do, the grass outside does… even yeast does. The origin of homeobox genes is ancient, definitely pre-dating the origin of animals. This 180-base-pair homeobox codes for a 60-residue chain known as the homeobox domain (or homeodomain). So the region of the gene is known as a homeobox, the region of the protein is the homeodomain. The explanation for why it is so conserved across organisms, through hundreds of millions of years of evolution, is that its function restricts its evolution. The homeobox domain binds DNA (or RNA), allowing a protein with a homeodomain to act in gene regulation. For example, these proteins can be used to turn genes on and off. It’s an invention of evolution that’s persisted through the origin of the fungi, plants, and us animals, and the homeobox itself hasn’t changed much at all. So there’s your definition of a homeobox gene. It isn’t a specific gene, it’s a huge and ancient group of genes that all contain the homeobox, a region of DNA that codes for a domain which can bind to DNA.

Every Hox gene is a homeobox gene, but not every homeobox gene is a Hox gene. The homeobox genes have diversified so much through evolutionary history that there are now distinct classes of them. The most famous is definitely the family of Hox genes. This is also where the terms come from. When scientists first discovered the homeobox domain, they found it because they were studying animals that had mutated Hox genes. These mutants often had body parts in the wrong place, and were described as “homeotic mutants”. When they identified the genes causing the mutations, they discovered that they all shared a common motif, so they named it the homeobox. This is one of the most incredible discoveries in biology, as they quickly realised that the homeobox is found in genes from humans, flies, jellyfish, daffodils, yeast, and so on. But the actual genes they had discovered were a distinct group of homeobox genes, which we now call the Hox genes. They definitely are homeobox genes, and they regulate other genes.

Think about the confusion here. Hox genes are a distinct family of homeobox genes. Scientists discovered the homeobox motif by investigating which genes caused homeotic mutations. What they had found were the Hox genes, so calling Hox genes homeotic is fine. But they didn’t understand at the time that the homeobox motif is found in many genes that aren’t Hox genes. Many homeobox genes have absolutely nothing to do with body parts growing in the right or wrong places. But when they named the homeobox, they only knew of the Hox genes they were discovering via the homeotic mutants. This is where almost all the confusion stems from. Despite being called homeobox genes, most don’t cause homeotic mutants if modified. The Hox genes, a specific family of homeobox genes, are great examples of genes that can cause homeotic mutants.

In us bilaterian animals, one of the main roles of the Hox genes is to specify anteroposterior identity to your body. It’s a complicated system, but we’ll keep it simple. The Hox genes play a role in determining which body parts grow where on the body. So by messing with them you can make limbs grow in the wrong places. But there are plenty of other non-Hox homeobox genes. There are entirely different families with entirely different roles. The Hox genes control the body plan along the anterior to posterior axis in us bilaterian animals, but there’s still some uncertainty over their precise role in non-bilaterian animals. The Hox genes do appear to be unique to animals. You don’t find Hox genes in plants and fungi. They have homeobox genes, but not the Hox genes, which appear to have arisen very early in animal evolution (there is evidence that sponges had Hox genes too, but have since lost them).

We know so much about homeobox genes, especially the Hox cluster, that we could discuss it all day. The evolution of the Hox, ParaHox, and NK clusters is quite fascinating, as are the roles of these gene families in a developing animal. I’ll save these for future entries. Today’s point is mostly just an early-morning rant. Hox genes are homeobox genes as they contain the homeobox, but homeobox genes include Hox genes, ParaHox genes etc. The terms are not interchangeable. It’s such an easy mistake to make that it appears in books, academic websites, and helpful videos on YouTube. Just keep it in mind and focus on what exactly is being discussed. It’s not necessarily wrong to describe a mobile phone as technology, but the terms aren’t interchangeable. You can’t go around describing technology as mobile phones. It makes no sense to say, “the electron microscope is a wonderful mobile phone”. Homeobox and Hox genes work the same way. You can describe a Hox gene as a homeobox gene because that’s exactly what it is. But note that the terms aren’t interchangeable.

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I've only just started reading the Harry Potter series. I know, I know. One of my favourite things so far was the Weasley's clock in Chamber of Secrets. It's a clock that shows where people are and what they're doing rather than the time. I see programming as a form

I've only just started reading the Harry Potter series. I know, I know. One of my favourite things so far was the Weasley's clock in Chamber of Secrets. It's a clock that shows where people are and what they're doing rather than the time. I see programming as a form of modern magic, so why not build a technological Weasley clock?

My working Weasley clock uses a Raspberry Pi and LEGO. The clock itself is a black cardboard box with the design on top. The LEGO hand is connected to a LEGO Mindstorms motor, which a Python script on the Raspberry Pi controls via the BrickPi. The script receives location data from iOS or Android using the devices' native GPS features and IFTTT.

The words on the original design refer to different things for me. For example, when the hand is at "tailor" it means the person is at the shops. "Lost" means anywhere that isn't an obvious location or route to a destination on the clock.

It's not perfect yet but it works. I'll be uploading instructions to build your own when I'm happy with it.

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I've always found palaeontology fascinating, probably due to my love of dinosaurs from an early age. These days I have a different appreciation of palaeontology because of the fact that development evolves. I've met several people who believe that evo-devo (evolutionary developmental biology) is all about genomics and has little

I've always found palaeontology fascinating, probably due to my love of dinosaurs from an early age. These days I have a different appreciation of palaeontology because of the fact that development evolves. I've met several people who believe that evo-devo (evolutionary developmental biology) is all about genomics and has little to do with fossils these days. I don't think that's quite right.

Evolutionary developmental biology (evo-devo) is a discipline concerned with evolution, development, and the interplay between the two. An adult-centric view of evolution leaves some people imagining that changes in the form of an adult ancestor leads to a different adult descendent. But adults do not directly evolve into different types of adults. Instead, evolution of adult form takes place when egg-to-adult development is altered within an evolving lineage. The fact that development itself evolves has implications for our understanding of development itself, but also evolutionary theory. Evolution of developmental processes results in new morphologies, introduces developmental constraints or biases in evolution, and creates complex problems for our understanding of potentially homologous characters.

Many of the most important discoveries in evo-devo have occurred in the last twenty years, thanks largely to advances in molecular biology. It is common to find evo-devo research focusing on the evolution of developmental genetics and working with extant model organisms, but throughout its history evo-devo has also relied on the study of embryology, morphology and palaeontology. It is often said that evo-devo truly begun in the 1980s with the discovery of the homeobox genes. New doors may have opened, but scientists had considered and debated the interplay between evolution and development for over a century.

In Darwin’s time there were arguments that changes to development could play a role in evolution. In The Origin of Species (1859), Darwin describes evolution taking place due to slight changes introduced at different stages of development and in different parts of the body over millions of years. This point of view was repeated by other early Darwinists, including Thomas H. Huxley in Evidence as to Man's Place in Nature (1863). Clearly the connection between development and evolution isn't a new idea. In an 1860 letter to American botanist Asa Gray, Darwin wrote:

"Embryology is to me by far the strongest single class of facts in favour of change of form, & not one, I think, of my reviewers has alluded to this."

Molecular biology was non-existent for most of this history. The most obvious evidence of morphology evolving could be found in the fossil record. Palaeontology has clearly been of vital importance to evo-devo long before the discovery of the homeobox genes and the development of powerful tools that reveal the mechanisms of developmental genetics. A quick glance at the most recent evo-devo papers could suggest that the genetic and genomic approach has usurped palaeontology in evo-devo; that it had its time and was the best we could work with before molecular genetics. In reality, palaeontology is vitally important in today's evo-devo research and even aids the molecular and genomic approaches. There are some questions that may never have been answered relying on palaeontology alone, but the same can be said for the molecular approach. Evo-devo is a multidisciplinary endeavour.

Matt Smith working at the John Day Fossil Beds.

Despite being incomplete, the fossil record provides our only direct window to the body plans of extinct taxa. Without palaeontology we would not know of the existence of huge and diverse clades of organisms including the trilobites, the dinosaurs, and the bizarre body plans observed in the Cambrian strata. In rare cases palaeontology can actually provide genomic information too. A Neanderthal genome project is under way based on well-preserved fossil finds. Comparing the genomes of Homo sapiens and Pan troglodytes can reveal changes that have occurred on our lineage since the divergence from one another but that covers several million years of evolution. It's thought that information from the Neanderthal genome will identify which of these changes occurred since diverging from the Neanderthal lineage and may have played a role in making modern humans what they are today.

It is often claimed in the literature that preserved DNA will be impossible to recover in fossils older than approximately 100,000 years but the current record goes to a 1.12-times coverage draft genome from a horse bone dated to 560,000-780,000 years old. Unfortunately, this type of DNA preservation is unlikely to occur for extinct taxa that are of interest in many key evo-devo topics as they are usually hundreds of millions of years older. The remarkable ancient genomes being sequenced are very rare exceptions as the genomes of 99.9% of extinct organisms are forever lost. So if the fossil record can't provide many genomes for evo-devo scientists to work with, what can it provide instead? Is palaeontology simply the old-fashioned way to do evo-devo?

Phylogeny reconstruction

The fossil record can improve phylogenies by providing evidence of features along lineages of extant and extinct taxa. These fossils can fill gaps in phylogenies and reveal ancestral relationships that would otherwise by unknown. Phylogenies are concerned with the identification of speciation events and diverging lineages evolving independently but carrying homologous genes and other characters. The study of development (including its evolution) and phylogeny feed into each other. Our phylogenies inform our understanding of how development evolves, and discoveries in evo-devo can provide more informative data for use in phylogeny reconstruction.

The data for many modern phylogenies typically comes from extant taxa and statistical methods are used to predict tree topology and patterns of ancestry. But understanding the distribution of characters in extinct lineages leading to extant taxa allows us to polarise evolution and recognise patterns of evolution for features relevant to evo-devo. Understanding which lineages a character occurs in can inform our phylogenies and allow targeting of more informative extant taxa for analysis. Palaeontology can also help identify whether characters in extant taxa are homologous or convergently evolved, which is useful for phylogenies and evo-devo in general.

Molecular clock calibration

An important aspect of the interplay between development and evolution is the timing of evolutionary events including speciation events resulting in the origin of new taxa, the timing of characters gain and loss in extinct taxa, and extinction events. Some taxa have a tendency to be relatively well-preserved and are found in several strata. These are easier to date based on the rocks they are found in. But for taxa with incomplete fossil records, a molecular clock is required to date important times of divergence.

As useful as molecular clocks have been for taxa poorly represented in the fossil record, they still require palaeontological evidence as molecular clocks are calibrated using the divergence times of well-preserved fossil taxa (or sometimes geological events). There are four downsides to this approach:

We are unlikely to find the earliest member of a clade so statistical methods are used to infer the error limits of divergence.

This approach assumes that our phylogenies are correct. If tree topology is incorrect then nodes can shift forwards or backwards in time and ruin the calibration.

Fossils lie in sedimentary rocks, which cannot be radiometrically dated. Instead, the igneous rocks immediately above or below the sedimentary rocks are used. There is an uncertainty involved in correlating the sedimentary and igneous rocks that can result in over- or under-estimation of the divergence times.

The genes used must be orthologues, not paralogues, found in two taxa for which the fossil divergence time is estimated. The number of nucleotide changes that have occurred since divergence are calculated. This can be complicated by differences between taxa in the rates of nucleotide substitution and the possibility that the genes being compared are paralogues that evolved from orthologues after a divergence. An extremely careful choice of genes to be used is essential.

Understanding development

Some people assume that fossils and molecular data go hand-in-hand in other areas of evolutionary biology but not in evo-devo. In the fossil record, change over generations and between taxa is clear, but useful developmental evidence is rare. Nevertheless, palaeontology can be useful for evolutionary developmental biologists when constructing hypotheses using molecular data from living taxa as fossil evidence can constrain molecular hypotheses. Some studies on the development of digits in extant birds have suggested that their three digits are 1, 2 and 3 while others have suggested they are digits 2, 3 and 4. Fossils of extinct bird lineages and theropod dinosaurs constrain the molecular predictions to 1, 2 and 3. Fossils can help developmental biologists make sense of molecular data.

Despite developmental evidence being rare in the fossil record, it isn't non-existent. The development of individual fossil organisms is impossible to study but life histories have been described for some well-preserved fossil taxa including many trilobite species. Even fossils of ancient larvae and embryos are occasionally found, though these finds are typically limited to specific taxa and eras. With advanced imaging techniques, informative characters of these larvae and embryos may be discovered and be of use in evo-devo. New imaging techniques are uncovering fascinating details from adult fossils too. In 2012 Ma et al described the oldest tripartite brain in the fossil record, belonging to a stem-group arthropod that lived approximately 520 million years ago. Assuming reasonable preservation in the depth of a specimen, computed tomography or computed synchrotron and phase-contrast radiation X-ray tomography can be used to resolve soft tissue preservation in ancient fossils. In 2013, Tanaka et al were able to analyse the neuroanatomy of Alalcomenaeus sp., a Cambrian “great appendage” arthropod (see the image below). This research helps confirm Alalcomenaeus as a stem-group chelicerate. State-of-the-art imaging of Alalcomenaeus and Fuxianhuia protensa reveal that the brain configurations observed in the extant Chelicerata and Mandibulata had already evolved by the early Cambrian. With more advanced imaging techniques, important questions in evo-devo may be addressed by obtaining data from ancient nervous systems, larvae, and embryos.

Specific questions regarding origins

A layman's view might be that questions regarding ancient extinct taxa require answers from palaeontology and that developmental genetics and other molecular approaches are of more use when studying extant taxa. This is not always the case. Two of the most debated topics in evo-devo concern the origin of the metazoans and the description of the last bilaterian common ancestor (LBCA). These topics address truly ancient events and organisms but the fossil record is unfortunately incomplete and often uninformative on these topics. The best attempts so far at addressing these issues have involved reconstructing hypothetical ancestors using data from extant species by comparing genomes and developmental mechanisms, and using molecular data to reconstruct more accurate phylogenies.

Most reconstructions of features in important extinct basal taxa have relied heavily on the developmental genetics of living taxa. Comparisons of protostome and deuterostome genomes and development have generated most hypotheses regarding the LBCA. This is not a perfect approach, as there is a danger of mistaking homoplasy or homology. If a protostome and deuterostome possess homologous developmental genes used in patterning a shared structure, does that mean the structure is homologous? There is always the possibility that the genes themselves have been independently co-opted in both lineages.

The other approach, in the absence of desired fossils, is to use extant basal taxa as proxies when investigating major divergences in metazoan phylogenies. Sponges are often considered the most basal metazoans. Acoel flatworms are often considered the most basal bilaterians. But how representative are they? Sponges and acoel flatworms have been evolving along their own lineages for hundreds of millions of years. There is a risk that their genomes and morphologies may be too derived to be informative. If sponges possess genes or gene networks used by other metazoans for more complex development, it isn't clear whether or not the ancestor of all metazoans used the genes in a similar way to extant sponges. The development of extant sponges could be quite derived compared to the ancestor of all metazoans. Better fossil evidence could help determine how useful various extant basal taxa are as proxies.

Palaeontology often provides its most informative discoveries when highly unusual fossils are found. The Burgess Shale sponge Eiffelia globosa contains both hexaradiate and tetraradiate spicules, typical of calcarean and hexactinellid sponges, respectively. This information, combined with the molecular data suggesting that extant sponges are paraphyletic, allows us to learn more about sponge ancestry than was available through genomic information alone. Perhaps understanding ancient animal origins could be within our grasp if we were fortunate enough to find more unusually informative fossils. A single fossil can have a large effect on our view of ancient relationships and the timing of events. Another example of an unusually informative fossil is that of Kimberella, which appears to be a complex bilaterian existing in the Ediacaran. This suggests that the bilaterian radiation may have preceded the Cambrian explosion, which many have associated with evolution of the bilaterians.

Moving forward?

Much like evo-devo itself isn't a threat or replacement for the "modern synthesis" or ecological evolutionary biology, molecular techniques add to evo-devo rather than replace the role of palaeontology in the discipline. There are many questions in evo-devo that have only been answered due to palaeontology, and the same can be said for molecular techniques. Both approaches have proven their worth and both are used to aid each other. The role of palaeontology in evo-devo is as important today as it ever was, or perhaps more so with the use of the fossil record in calibrating molecular clocks, constraining molecular hypotheses, and providing increased taxon sampling for phylogenetic analysis. The very nature of evo-devo makes it a multidisciplinary endeavour with many areas of research complimenting each other. The way forward for both palaeontological and molecular approaches in evo-devo is clearly together. Being obsessed with evo-devo, I'm as fascinated by fossils as I am genomes. I'm following the development of new imaging techniques as keenly as the next generation of sequencing technologies. Palaeontology isn't old-fashioned, it's vital.

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Beautiful chickens is a simple Chrome extension for Twitter, which was requested by @EJWrites1. It replaces any mention of "beauty" with "chickens" while browsing Twitter. It doesn't affect other websites.

Beautiful chickens is a simple Chrome extension for Twitter, which was requested by @EJWrites1. It replaces any mention of "beauty" with "chickens" while browsing Twitter. It doesn't affect other websites.

I recently had a discussion where the word “homology” was thrown around very loosely by someone who should probably know better. Those who have at least heard of the word might think it has something do with things being similar. Those with an interest in biology, especially evolutionary biology, probably realise it’s more complicated than superficial similarity. Sadly, I see the word used in various ways all the time and thought I’d share some thoughts.

The word “homology” has been used for over 150 years and has meant different things to different biologists, with similarity of characters being the common theme. Most modern biologists use the word to refer to similarity that is due to common ancestry: two characters are homologous if they are derived from the same ancestral character in their most recent common ancestor. Any characters that exist in related lineages can be assessed for homology, including genes, chromosomes, genomes, cells, limbs, regions of the brain, behaviours, and the developmental programmes that result in these characters. Ancestors are rarely available for examination so homology is usually an evolutionary hypothesis rather than a direct observation.

Even among biologists, the correct definition of homology is still occasionally an issue. Some researchers write of “functional homology” when describing similar functions of traits. Some examples of supposed “functional homology” will be truly homologous in the sense of common ancestry, while others will be non-homologous but convergently similar. In some of the literature, homology still refers to characters that are merely similar, regardless of ancestry. If homology is defined by similarities, there may be a gradient of homology for any given character. Some characters are presumably more similar than others. If they are a slightly similar, are they only slightly homologous? If they are very similar, are they very homologous? Where do we draw the line? When do two similar traits become similar enough to warrant being described as homologous? This subjective issue is avoided entirely when common ancestry is used to define homology. We may not know for certain if two characters are homologous, but they either are or aren’t. This approach makes the concept of homology simpler to define and have researchers agree upon, but requires rigorous investigation to determine if homology exists in any given character.

Image taken from Hall (2003). This image demonstrates the homologous and homoplastic relationships of a character, C. B represents the plesiomorphic state of the character. The Cs in clade 1 are homologous because C already existed in the most recent common ancestor of the two lineages. The same situation is observed in clade 2. But when comparing Cs between clades 1 and 2, the relationship is homoplastic as C did not exist in the most recent common ancestor (3). Lineages 1 and 2 independently evolved the C character from the ancestral B character.

Understanding ancestral relationships in any kind of comparative biology usually involves recognising the differences between homology and homoplasy (as in the figure above). Homology is similarity because of common descent and ancestry. Homoplasy is similarity because of independent convergent evolution. Definitions must be clear. Some related characters are orthologues, arising from lineages splitting and diverging. Others are paralogues, arising from gene duplication. Some genes can also be xenologues if they have arisen from horizontal gene transfer. Understanding homology is essential in comparative biology because of the practical applications of such knowledge. Homology can be used in constructing character matrices for phylogenetic analyses. Also, finding functionally equivalent orthologues of human genes in model organisms has an important role in medical research. A geneticist studying fly orthologues of our genes needs to be sure that he/she has the correct homologue. The same can be said for a medical researcher studying human orthologues in mice that may influence the likelihood of getting cancer or Alzheimer’s disease. It is vital that evolutionary biologists understand what is truly homologous.

One level of homology is that of genes. When genes are replicated, their daughters can undergo independent evolutionary change much like individual organisms can. Phylogenetic analysis is as possible on individual genes as it is on species. Because genes can replicate, either within the same genome (paralogy) or because of a speciation event (orthology), divergent genes can evolve independently but they are homologous due to their common ancestry. Homology doesn’t only occur at the level of genes. Over generations, phenotypes can change considerably. Morphological characters in different species are homologous if they arose from an ancestral state. They may be highly derived and superficially unrecognisable as homologues, they may even have novel functions, but the modern definition of homology is concerned with their relationship with one another rather than superficial or functional similarity. After agreeing on the concept of homology by common ancestry, it’s a relatively simple concept to understand when considering a single level, e.g. a morphological character or a gene. Homology is simply the continuation of characters. The complications arise when the genetic and morphological levels of homology are integrated. Developmental genetics involves understanding the relationship between morphological characters and their genetic basis.

The modern evolutionary synthesis reconciled genetics and the evolution of morphology (and other phenotypic traits such as physiology, behaviour etc) by natural selection. But before the influence of modern evo-devo, developmental was relatively poorly understood compared to traditional genetics and was seen as a black box that transforms the genetic information into three-dimensional, morphological structures. In the last two decades, evo-devo has replaced this black box development with an appreciation of the mechanisms responsible for generating morphological structures from genetic information. How genes are used in development is as important as what genes are available, and lineage-specific differences can come about due to changes in spatial or temporal expression of genes as well as by the evolution of the genes themselves. Development is complex, often involving many genes influencing the expression of each other, and highlights important information about homology. Developmental mechanisms may be conserved even if complete structures don’t form in some species (rudiments and vestiges) and can differ even for structures that are homologous. This suggests that there is a third level to consider, between genes and morphology (or other characters of the phenotype). Can entire gene regulatory networks be homologous? Does this have implications for the relationship between genes and morphology? How can we identify true homologues if there is a disassociation between the genotype and the phenotype? These are questions I find fascinating.

Disassociation between genotype and phenotype

Wagner argued that homology at the levels of genetics and morphology are similar, as morphological characters are equivalent to genetic loci. Just as there may be different alleles present for a gene in a population, there may be different states for a morphological character. A gene and a morphological character can be duplicated during a speciation event. The gene would be an orthologue. The morphological equivalent would be a bat’s wing and a cat’s anterior legs, which are homologous characters in related species. But duplications can also occur within a species. Gene duplication can create paralogous genes. These genes are certainly homologous and have a common ancestor, but both descendents occur in the same genome. The morphological equivalent would be when morphological characters become repeated, such as teeth or extra limbs.

It is reasonable to expect that the genetics of a morphological character can evolve and thus evolve the morphological character itself. Therefore, if a morphological character has evolved, it must be because the underlying genetics have evolved. When homology is applied to phenotypic characters (e.g. morphological structures, behaviours, modes of communication), those characters existed in the last common ancestor. So both levels can be thought of as equivalents of one another and both are relatively simple to appreciate conceptually. Indeed, it isn’t surprising that similar features persist over evolutionary time and in multiple species (homology), especially if the developmental basis of that feature has also been conserved. It also isn’t surprising that different selection pressures can bring about similar features in organisms that do not share a most recent common ancestor (homoplasy). The more surprising observation is that homologous features can be formed from non-homologous developmental processes, and homologous developmental processes can be found forming non-homologous features. It is the relationship between the two levels that complicates our understanding and makes this such a strange issue.

Thinking at two levels of homology (morphological characters and the genes involved in their development), it appears to be a paradox. It doesn’t make intuitive sense that homologous morphological characters are brought about by the expression of non-homologous genes. It is not difficult to imagine a situation where this paradox causes two biologists to disagree over the supposed homology of a morphological character. If one relied on comparing gene expression between species, and the other relied on bone structure or another morphological feature, the paradox could confuse matters. A careful approach considering multiple lines of evidence is clearly required, but which lines of evidence? Is it as simple as genes vs morphology? The relationship between genotype and phenotype is remarkably complex. Developmental processes can evolve independently yet result in the same phenotypic character. This disassociation between the genotype and phenotype has been referred to as “phenotypic drift” or “developmental system drift”. Such a disassociation through evolution can make the search for homologous characters difficult. It can be easy to mistake morphological characters as being homologous just because homologous genes are involved in their development. Inversely, truly homologous morphological characters may be overlooked if it is realised that their genetic or developmental bases are different. It is also important to remember that genes do not operate in isolation. Researchers must consider networks of genes and the role they play in the development of morphological structures.

Homologous genes and non-homologous phenotypic characters

There are many examples of homologous genes being used in the development of non-homologous phenotypic characters. Most developmental regulatory genes of metazoans are more ancient than their developmental roles are. Homeobox-containing genes predate the origin of metazoans yet are often involved in patterning phenotypic structures that are unique to metazoans. Clearly their roles in development have evolved over time with new roles being gained and old roles being lost in some lineages. The segmentation in Drosophila melanogaster, Schistocerca americana and Aphidius ervi is putatively homologous, yet there are genes essential for segmentation in the fruit fly that play an entirely different role in the locust and wasp. The genes ushi tarazu and even-skipped are pair-rule genes in the fly, which divide gene expression into half-segments of the embryo. In the locust and wasp, these genes are involved in the development of the central nervous system rather than body segmentation.

It is a recurring theme that homologous transcription factors can have different roles in different taxa. Orthologues of distal-less, engrailed, and orthodenticle in echinoderms pattern different morphological features than they do in arthropods and chordates. In arthropods and chordates, distal-less is expressed during limb outgrowth and plays a role in proximodistal patterning, engrailed is involved in neurogenesis in the central nervous system, and orthodenticle has a role in the specification of anterior structures. In most echinoderms, distal-less and orthodenticle are expressed in the podia and engrailed is involved in skeletogenesis. But evolution has altered the expression and roles of these genes even among echinoderms. In the Asteroidea (sea stars), distal-less is expressed in the larval brachiolar arms. In the Echinoidea (sea urchins), engrailed is involved in rudiment invagination. In the Holothuroidea (sea cucumbers), orthodenticle is expressed in the larval ciliated band. These changes in expression and role correlate with novel morphological features such as brachiolar complex of sea star larva or the sea urchin’s rudiment ectoderm invagination. Pre-existing genes have been co-opted for new roles in echinoderms.

Regulatory genes rarely have one role in a developing organism. The Notch signalling pathway is highly conserved and found in all metazoans. In Drosophila melanogaster, it is used in the development of wings, ommatidia, and bristles. These morphological structures are clearly not homologous, yet their development has common genetic features. Throughout the Metazoa, the Notch pathway can be found in the development of characters as diverse as feathers and T-lymphocytes. True conservation also occurs, such as the Hox genes and their role in patterning the anteroposterior axis in animals as different as fruit flies and humans. But these genes often have multiple roles. Although one role can be highly conserved, often there are divergent unique roles for these genes in different lineages.

Non-homologous genes and homologous phenotypic characters

Instead of homologous genes having roles in producing non-homologous morphologies, some homologous morphological characters are produced by non-homologous genes. Sex-lethal is a master regulatory gene that controls sex determination in Drosophila melanogaster. In other dipterans such Ceratitis capitata and Musca domestica, Sex-lethal exists but isn’t used in sex determination and is expressed during a different stage of development. Phylogenetic analysis suggests that the role in sex determination is the derived condition. Where even-skipped was co-opted to be used in the development of a novel morphological feature, Sxl has become involved in a developmental process that already existed. Sex determination in the Drosophila lineage existed before Sxl.

In most tetrapods, programmed cell death separates digit primordia during embryonic development. This creates interdigital space, allowing the primordia to develop into individual digits. In urodele amphibians, differential growth of the digits separates them, without apoptosis creating interdigital space. As a morphological feature, the digits of urodeles and other tetrapods are homologous. But the developmental processes and the genetics controlling those processes are not homologous. This phenomenon of homologous phenotypes being generated by non-homologous developmental processes is not restricted to adult morphology. In vertebrate embryos, the gastrula stage is considered to be homologous. However, it is found that very different developmental processes produce the gastrula in different vertebrate taxa.

Levels of homology

By revealing that development itself evolves, evo-devo implies that homology should be understood in a hierarchical fashion as there are several levels of homology. Homology at one level might not correspond to homology at other levels. As already discussed, two species may have homologous limbs, but the developmental processes that produce the limb, or the genetic cascades underlying those processes, may be different. For example, formation of the neural crest can occur by delamination or by cavitation, and gastrulation can occur via a blastodisc or a blastopore.

Some researchers have interpreted similar patterns of regulatory gene expression alone as evidence that morphological structures are homologous. This ignores the idea that homology may exist at several levels and it limits the evidence to a single source. Assuming that similar gene expression identifies homologous structures ignores the evolutionary histories of the structures and the regulatory genes. What exactly is homologous in a given example? The genes? Their expression patterns? Their developmental roles? The morphological structures that arise because of them? Because some of these levels can be homologous while others aren’t, mistakes can be made when expression data alone is used to assign homology to structures. At least three levels of homology and homoplasy must be considered: genes, developmental processes, and the resulting phenotypic character.

How can a morphological character (like segmentation) be homologous if different genes are involved? The answer lies in understanding developmental genetics and gene regulatory networks. Developmental processes can create different features in different organisms because they can be co-opted for new roles and old pathways can resurface or remain unexpressed, perhaps to be co-opted in the future. Wagner proposed that the homology of morphological characters is related to the continuity of gene regulatory networks (GRNs) rather than the expression of individual homologous genes. He refers to these networks as “character identity networks” (ChINs) and argues that they are what enables the execution of character-specific developmental programmes. In insect segmentation, more variation is seen in the homologous genes that are further upstream than downstream. Gap genes and pair-rule genes are higher in the segmentation hierarchy yet show more variation than lower genes such as the segment-polarity genes. Only the Diptera possess the gap gene bicoid and not even all members of the Diptera. Other segmented insects use different genes at this level of the segmentation hierarchy. But downstream GRNs are more conserved between taxa. Most if not all insects use engrailed and wingless as segment-polarity genes.

Generalising the insect segmentation data, Wagner argued that it is the most downstream regulatory networks, the ChINs, controlling the development of morphological characters that specifies the identity of the character. If homologous morphological structures are controlled by homologous ChINs, this would explain the paradoxical relationship between morphology and genes. The use of different genes in developmental programmes for homologous morphological characters could be explained by homologous ChINs co-opting different individual genes (or pathways) independently. A kernel is a highly conserved GRN. The term ChIN is instead concerned with GRNs that execute a character-specific developmental programme. Some kernels will be ChINs, but not all, as both terms were created for different reasons. One is concerned with conservation and age, the other with the relationship between the GRN and its ability to program character identity. Homologous ChINs can be very conserved, but can also co-opt different transcription factors in their regulation.

Let's wrap this up

The complex evolutionary relationship between genotype and phenotype provides two important messages. Firstly, as useful as gene expression data has been, it isn’t sufficient for diagnosing homologous morphological structures. Notch signalling doesn’t suggest that our T-cells and Drosophila eyes are homologous. Regulatory genes have multiple expression domains and play multiple roles in development. Also, it has been assumed that novel structures require novel genes or at least alleles. But how could new alleles or genes become established in a population before they produce an advantageous phenotype? Developmental genes and their ability to have multiple roles suggests an answer to this question. Genes can already exist in a population as new roles evolve and provide fitness advantages for individuals, and potentially the population, given time. Because developmental genes gain and lose roles, some morphological novelties presumably arise by co-opting pre-existing developmental genes for new roles. The echinoderm morphological novelties mentioned earlier provide a good example. At the same time, it’s important not to consider the disassociation between genotype and phenotype as a hindrance to investigation or as noise that stops us from identifying truly homologous characters. There is a lot to learn from studying homology. This phenomenon provides an opportunity to understand how morphological novelties come about and the role co-option plays.

Beyond any confusion caused by multiple levels of homology, there are other common issues in the literature that quite frankly get on my nerves. The nomenclature of genes often makes it difficult. Dlx-2 in Xenopus is not orthologous with Dlx-2 in zebrafish. This example refers to paralogous genes that duplicated before the divergence that led to Xenopus and zebrafish. Even more confusing is when paralogous genes evolve by duplication in independent lineages. It can be extremely difficult to tell which of the duplicates corresponds to the ancestral gene. The homologous gene may have been lost, leaving only the paralogues. Clearly, relying on just one line of evidence isn’t always sufficient for identifying homology. Another major problem is the notion of “functional homology”, which confuses similarity due to common ancestry with similarity due to functional convergence. The functions of homologous genes can diverge from their original functions, or converge on the functions of unrelated genes. Both of these possibilities could confuse a researcher relying only on gene expression patterns as evidence of homology. Clearly homologous structures and genes can have different functions, so similarity of function is not a valid criterion for identifying homology, yet “functional homology” is still occasionally used in the literature. The solution to these two problems is to constantly consider phylogenetics and evolutionary histories when comparing gene expression data. By reconstructing the gene family in all the species being compared, the timing of gene duplications can be calculated relative to the divergences of the species. This approach should improve the likelihood of identifying true orthologues so that only their gene expression patterns are compared.

A third problem that is more difficult to solve (and happens to be one of my favourite biological topics) is the phenomenon of co-option. As discussed, this can lead to the recruitment of orthologous genes to be expressed in non-homologous structures during development. Arthropods, echinoderms, and chordates express distal-less in the distal region of their appendages during their outgrowth, but the structures themselves aren’t homologous. It has become important to distinguish the difference between homology of genes, developmental mechanisms, and morphological structures or other phenotypic characters. To use homology in comparative biology, researchers should observe that homology can exist at different levels and that true homology concerns the evolutionary histories of characters, rather than any general or functional similarity. This approach to homology should be used consistently in studies, whether studying gene expression, developmental mechanisms, or morphological structures. At least that’s what I think.

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The Brexit (Leave) campaign has a flotilla entering the Thames. Seriously. We've reached that point. Brexit Floater is a simple Chrome extension for Twitter, which was requested by @GirlOnTheNet. It replaces any mention of "flotilla" with "floater" while browsing Twitter. It doesn't affect other websites.